Package picard.sam.markduplicates.util
Class LibraryIdGenerator
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- picard.sam.markduplicates.util.LibraryIdGenerator
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public class LibraryIdGenerator extends Object
A class to generate library Ids and keep duplication metrics by library IDs.
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Constructor Summary
Constructors Constructor Description LibraryIdGenerator(htsjdk.samtools.SAMFileHeader header)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addMetricsByLibrary(String library, DuplicationMetrics metrics)
htsjdk.samtools.util.Histogram<Double>
getDuplicateCountHist()
short
getLibraryId(htsjdk.samtools.SAMRecord rec)
Get the library ID for the given SAM record.Map<String,Short>
getLibraryIdsMap()
static String
getLibraryName(htsjdk.samtools.SAMFileHeader header, htsjdk.samtools.SAMRecord rec)
Gets the library name from the header for the record.DuplicationMetrics
getMetricsByLibrary(String library)
Map<String,DuplicationMetrics>
getMetricsByLibraryMap()
htsjdk.samtools.util.Histogram<Double>
getNonOpticalDuplicateCountHist()
long
getNumberOfOpticalDuplicateClusters()
htsjdk.samtools.util.Histogram<Double>
getOpticalDuplicateCountHist()
htsjdk.samtools.util.Histogram<Short>
getOpticalDuplicatesByLibraryIdMap()
static String
getReadGroupLibraryName(htsjdk.samtools.SAMReadGroupRecord readGroup)
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Method Detail
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getMetricsByLibraryMap
public Map<String,DuplicationMetrics> getMetricsByLibraryMap()
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getOpticalDuplicatesByLibraryIdMap
public htsjdk.samtools.util.Histogram<Short> getOpticalDuplicatesByLibraryIdMap()
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getDuplicateCountHist
public htsjdk.samtools.util.Histogram<Double> getDuplicateCountHist()
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getNonOpticalDuplicateCountHist
public htsjdk.samtools.util.Histogram<Double> getNonOpticalDuplicateCountHist()
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getOpticalDuplicateCountHist
public htsjdk.samtools.util.Histogram<Double> getOpticalDuplicateCountHist()
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getReadGroupLibraryName
public static String getReadGroupLibraryName(htsjdk.samtools.SAMReadGroupRecord readGroup)
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getLibraryName
public static String getLibraryName(htsjdk.samtools.SAMFileHeader header, htsjdk.samtools.SAMRecord rec)
Gets the library name from the header for the record. If the RG tag is not present on the record, or the library isn't denoted on the read group, a constant string is returned.
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getLibraryId
public short getLibraryId(htsjdk.samtools.SAMRecord rec)
Get the library ID for the given SAM record.
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getMetricsByLibrary
public DuplicationMetrics getMetricsByLibrary(String library)
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addMetricsByLibrary
public void addMetricsByLibrary(String library, DuplicationMetrics metrics)
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getNumberOfOpticalDuplicateClusters
public long getNumberOfOpticalDuplicateClusters()
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